org.sbml.jsbml.util.compilers

Class MathMLCompiler

java.lang.Object

org.sbml.jsbml.util.compilers.MathMLCompiler

All Implemented Interfaces:

ASTNodeCompiler

Direct Known Subclasses:

HTMLFormula

Deprecated.

use MathMLXMLStreamCompiler instead.

@Deprecated
public class MathMLCompiler
extends java.lang.Object
implements ASTNodeCompiler

With this compiler, an ASTNode can be transformed into a MathML string.

Since:

0.8

Version:

$Rev$

Author:

Andreas Dräger

Field Summary

Fields

Modifier and Type	Field and Description
private org.w3c.dom.Document	document Deprecated. XML document for the output.
private org.w3c.dom.Element	lastElementCreated Deprecated. The last top Element that has been created in the previous step.
private int	level Deprecated. The SBML level to be used in this class.

Constructor Summary

Constructors

Constructor and Description
MathMLCompiler() Deprecated.
MathMLCompiler(ASTNode ast) Deprecated.

Method Summary

Modifier and Type	Method and Description
ASTNodeValue	abs(ASTNode value) Deprecated. The absolute value represented by the given ASTNode.
ASTNodeValue	and(java.util.List<ASTNode> values) Deprecated.
ASTNodeValue	arccos(ASTNode value) Deprecated.
ASTNodeValue	arccosh(ASTNode value) Deprecated.
ASTNodeValue	arccot(ASTNode value) Deprecated.
ASTNodeValue	arccoth(ASTNode value) Deprecated.
ASTNodeValue	arccsc(ASTNode value) Deprecated.
ASTNodeValue	arccsch(ASTNode value) Deprecated.
ASTNodeValue	arcsec(ASTNode value) Deprecated.
ASTNodeValue	arcsech(ASTNode value) Deprecated.
ASTNodeValue	arcsin(ASTNode value) Deprecated.
ASTNodeValue	arcsinh(ASTNode value) Deprecated.
ASTNodeValue	arctan(ASTNode value) Deprecated.
ASTNodeValue	arctanh(ASTNode value) Deprecated.
ASTNodeValue	ceiling(ASTNode value) Deprecated.
ASTNodeValue	compile(CallableSBase variable) Deprecated.
ASTNodeValue	compile(Compartment c) Deprecated.
ASTNodeValue	compile(double mantissa, int exponent, java.lang.String units) Deprecated. Creates an ASTNodeValue that represents a real number in scientific notation, i.e., mantissa * 10^exponent, and the given units.
ASTNodeValue	compile(double real, java.lang.String units) Deprecated.
ASTNodeValue	compile(int integer, java.lang.String units) Deprecated.
ASTNodeValue	compile(java.lang.String name) Deprecated. A compiler will also have to deal with a name.
ASTNodeValue	cos(ASTNode value) Deprecated.
ASTNodeValue	cosh(ASTNode value) Deprecated.
ASTNodeValue	cot(ASTNode value) Deprecated.
ASTNodeValue	coth(ASTNode value) Deprecated.
private ASTNodeValue	createApplyNode(org.w3c.dom.Node tag, ASTNodeValue... childNodes) Deprecated.
private ASTNodeValue	createApplyNode(org.w3c.dom.Node tag, java.util.List<ASTNode> childNodes) Deprecated. Creates an apply Node with the given tag Node as its child and ASTNodeValues on the same level as the tag Node .
private ASTNodeValue	createApplyNode(java.lang.String tagName, ASTNode... childNodes) Deprecated.
private ASTNodeValue	createApplyNode(java.lang.String tagName, ASTNodeValue... childNodes) Deprecated.
private ASTNodeValue	createApplyNode(java.lang.String tagName, java.util.List<ASTNode> childNodes) Deprecated. Creates a Node with the tag "apply" and adds the given Node as its child.
private ASTNodeValue	createCiElement(java.lang.String name) Deprecated.
private org.w3c.dom.Element	createCnElement(double mantissa, int exponent, java.lang.String units) Deprecated.
private org.w3c.dom.Element	createCnElement(java.lang.Number value, java.lang.String units) Deprecated.
private ASTNodeValue	createConstant(java.lang.String tagName) Deprecated. Creates an ASTNodeValue with the single node as defined by the tagName.
private org.w3c.dom.Element	createCSymbol(java.lang.String name, java.lang.String definitionURI) Deprecated.
ASTNodeValue	csc(ASTNode value) Deprecated.
ASTNodeValue	csch(ASTNode value) Deprecated.
ASTNodeValue	delay(java.lang.String delayName, ASTNode x, ASTNode delay, java.lang.String timeUnit) Deprecated. Evaluates delay functions.
ASTNodeValue	eq(ASTNode left, ASTNode right) Deprecated. Equal.
ASTNodeValue	exp(ASTNode value) Deprecated.
ASTNodeValue	factorial(ASTNode value) Deprecated.
ASTNodeValue	floor(ASTNode value) Deprecated.
ASTNodeValue	frac(ASTNode numerator, ASTNode denominator) Deprecated. Fraction of two ASTNodes
ASTNodeValue	frac(int numerator, int denominator) Deprecated. A fraction of two int values.
ASTNodeValue	function(FunctionDefinition functionDefinition, java.util.List<ASTNode> args) Deprecated.
ASTNodeValue	function(java.lang.String functionDefinitionName, java.util.List<ASTNode> args) Deprecated.
ASTNodeValue	geq(ASTNode left, ASTNode right) Deprecated. Greater equal.
ASTNodeValue	getConstantAvogadro(java.lang.String name) Deprecated. Creates an ASTNodeValue that represent's Avogadro's number.
ASTNodeValue	getConstantE() Deprecated.
ASTNodeValue	getConstantFalse() Deprecated.
ASTNodeValue	getConstantPi() Deprecated.
ASTNodeValue	getConstantTrue() Deprecated.
org.w3c.dom.Document	getDocument() Deprecated.
int	getLevel() Deprecated.
ASTNodeValue	getNegativeInfinity() Deprecated.
ASTNodeValue	getPositiveInfinity() Deprecated.
ASTNodeValue	getRateOf(java.lang.String name) Deprecated.
ASTNodeValue	gt(ASTNode left, ASTNode right) Deprecated. Greater than.
ASTNodeValue	implies(java.util.List<ASTNode> values) Deprecated. Returns the logical implies between two ASTNode.
private void	init() Deprecated. Re-initializes the Document object belonging to this class.
ASTNodeValue	lambda(java.util.List<ASTNode> values) Deprecated. The body of a FunctionDefinition.
ASTNodeValue	leq(ASTNode left, ASTNode right) Deprecated. Less equal.
ASTNodeValue	ln(ASTNode value) Deprecated. Natural logarithm.
ASTNodeValue	log(ASTNode value) Deprecated. Logarithm of the given value to base 10.
ASTNodeValue	log(ASTNode base, ASTNode value) Deprecated. Logarithm of the given value to the given base.
ASTNodeValue	lt(ASTNode left, ASTNode right) Deprecated. Less than.
ASTNodeValue	max(java.util.List<ASTNode> values) Deprecated. Returns the maximum of the values.
ASTNodeValue	min(java.util.List<ASTNode> values) Deprecated. Returns the minimum of the values.
ASTNodeValue	minus(java.util.List<ASTNode> values) Deprecated. Subtraction.
ASTNodeValue	neq(ASTNode left, ASTNode right) Deprecated. Not equal.
ASTNodeValue	not(ASTNode value) Deprecated.
ASTNodeValue	or(java.util.List<ASTNode> values) Deprecated.
ASTNodeValue	piecewise(java.util.List<ASTNode> values) Deprecated.
ASTNodeValue	plus(java.util.List<ASTNode> values) Deprecated.
ASTNodeValue	pow(ASTNode base, ASTNode exponent) Deprecated.
ASTNodeValue	quotient(java.util.List<ASTNode> values) Deprecated. Returns the quotient of the division of the values.
ASTNodeValue	rem(java.util.List<ASTNode> values) Deprecated. Returns the remainder of the division of the values.
void	reset() Deprecated. Allows to re-use this object to compile another ASTNode.
ASTNodeValue	root(ASTNode rootExponent, ASTNode radiant) Deprecated.
private ASTNodeValue	root(ASTNodeValue rootExponent, ASTNode radiant) Deprecated.
ASTNodeValue	root(double rootExponent, ASTNode radiant) Deprecated.
ASTNodeValue	sec(ASTNode value) Deprecated.
ASTNodeValue	sech(ASTNode value) Deprecated.
ASTNodeValue	selector(java.util.List<ASTNode> nodes) Deprecated.
private void	setLevel(int level) Deprecated.
ASTNodeValue	sin(ASTNode value) Deprecated.
ASTNodeValue	sinh(ASTNode value) Deprecated.
ASTNodeValue	sqrt(ASTNode value) Deprecated. Square root.
ASTNodeValue	symbolTime(java.lang.String time) Deprecated. The simulation time.
ASTNodeValue	tan(ASTNode value) Deprecated.
ASTNodeValue	tanh(ASTNode value) Deprecated.
private ASTNodeValue	times(ASTNodeValue... values) Deprecated. Convenient method to perform internal changes.
ASTNodeValue	times(java.util.List<ASTNode> values) Deprecated. Product of all given ASTNodes.
java.lang.String	toMathML(boolean omitXMLDeclaration, boolean indenting, int indent) Deprecated.
ASTNodeValue	uMinus(ASTNode value) Deprecated. Unary minus, i.e., negation of the given ASTNode.
private ASTNodeValue	uMinus(ASTNodeValue value) Deprecated.
ASTNodeValue	unknownValue() Deprecated. Dealing with a malformed ASTNode.
ASTNodeValue	vector(java.util.List<ASTNode> nodes) Deprecated. Dealing with a vector.
private java.lang.String	writeName(java.lang.Object name) Deprecated. Converts the given Object into a String.
ASTNodeValue	xor(java.util.List<ASTNode> values) Deprecated. Exclusive or.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

document

private org.w3c.dom.Document document

Deprecated.

XML document for the output.

lastElementCreated

private org.w3c.dom.Element lastElementCreated

Deprecated.

The last top Element that has been created in the previous step.

level

private int level

Deprecated.

The SBML level to be used in this class.

Constructor Detail

MathMLCompiler

public MathMLCompiler()
               throws javax.xml.stream.XMLStreamException

Deprecated.

Throws:

javax.xml.stream.XMLStreamException

MathMLCompiler

public MathMLCompiler(ASTNode ast)
               throws javax.xml.stream.XMLStreamException,
                      SBMLException

Deprecated.

Parameters:

ast -

Throws:

javax.xml.stream.XMLStreamException

SBMLException

Method Detail

abs

public ASTNodeValue abs(ASTNode value)
                 throws org.w3c.dom.DOMException,
                        SBMLException

Deprecated.

Description copied from interface: ASTNodeCompiler

The absolute value represented by the given ASTNode.

Specified by:

abs in interface ASTNodeCompiler

Parameters:

value - Must be interpretable as a Number.

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

and

public ASTNodeValue and(java.util.List<ASTNode> values)
                 throws org.w3c.dom.DOMException,
                        SBMLException

Deprecated.

Specified by:

and in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

arccos

public ASTNodeValue arccos(ASTNode value)
                    throws org.w3c.dom.DOMException,
                           SBMLException

Deprecated.

Specified by:

arccos in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

arccosh

public ASTNodeValue arccosh(ASTNode value)
                     throws org.w3c.dom.DOMException,
                            SBMLException

Deprecated.

Specified by:

arccosh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

arccot

public ASTNodeValue arccot(ASTNode value)
                    throws org.w3c.dom.DOMException,
                           SBMLException

Deprecated.

Specified by:

arccot in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

arccoth

public ASTNodeValue arccoth(ASTNode value)
                     throws org.w3c.dom.DOMException,
                            SBMLException

Deprecated.

Specified by:

arccoth in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

arccsc

public ASTNodeValue arccsc(ASTNode value)
                    throws org.w3c.dom.DOMException,
                           SBMLException

Deprecated.

Specified by:

arccsc in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

arccsch

public ASTNodeValue arccsch(ASTNode value)
                     throws org.w3c.dom.DOMException,
                            SBMLException

Deprecated.

Specified by:

arccsch in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

arcsec

public ASTNodeValue arcsec(ASTNode value)
                    throws org.w3c.dom.DOMException,
                           SBMLException

Deprecated.

Specified by:

arcsec in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

arcsech

public ASTNodeValue arcsech(ASTNode value)
                     throws org.w3c.dom.DOMException,
                            SBMLException

Deprecated.

Specified by:

arcsech in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

arcsin

public ASTNodeValue arcsin(ASTNode value)
                    throws org.w3c.dom.DOMException,
                           SBMLException

Deprecated.

Specified by:

arcsin in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

arcsinh

public ASTNodeValue arcsinh(ASTNode value)
                     throws org.w3c.dom.DOMException,
                            SBMLException

Deprecated.

Specified by:

arcsinh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

arctan

public ASTNodeValue arctan(ASTNode value)
                    throws org.w3c.dom.DOMException,
                           SBMLException

Deprecated.

Specified by:

arctan in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

arctanh

public ASTNodeValue arctanh(ASTNode value)
                     throws org.w3c.dom.DOMException,
                            SBMLException

Deprecated.

Specified by:

arctanh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

ceiling

public ASTNodeValue ceiling(ASTNode value)
                     throws org.w3c.dom.DOMException,
                            SBMLException

Deprecated.

Specified by:

ceiling in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

compile

public ASTNodeValue compile(Compartment c)

Deprecated.

Specified by:

compile in interface ASTNodeCompiler

Returns:

compile

public ASTNodeValue compile(double mantissa,
                            int exponent,
                            java.lang.String units)

Deprecated.

Description copied from interface: ASTNodeCompiler

Creates an ASTNodeValue that represents a real number in scientific notation, i.e., mantissa * 10^exponent, and the given units.

Specified by:

compile in interface ASTNodeCompiler

Parameters:

mantissa - The number to be multiplied with ten to the power of the given exponent.

exponent - The exponent for the multiplier ten.

units - The identifier of the units object associated with the number represented by this element. Can be null if no units have been defined.

Returns:

compile

public ASTNodeValue compile(double real,
                            java.lang.String units)

Deprecated.

Specified by:

compile in interface ASTNodeCompiler

units - A String representing the Unit of the given number. This can be the identifier of a UnitDefinition in the model or a literal in Kind. Can be null if no units have been defined.

Returns:

compile

public ASTNodeValue compile(int integer,
                            java.lang.String units)

Deprecated.

Specified by:

compile in interface ASTNodeCompiler

units - A String representing the Unit of the given number. This can be the identifier of a UnitDefinition in the model or a literal in Kind. Can be null if no units have been defined.

Returns:

compile

public ASTNodeValue compile(CallableSBase variable)

Deprecated.

Specified by:

compile in interface ASTNodeCompiler

Returns:

compile

public ASTNodeValue compile(java.lang.String name)

Deprecated.

Description copied from interface: ASTNodeCompiler

A compiler will also have to deal with a name. The meaning of this can be various. For instance, the name may refer to a Species in the system. In case of numerical computation, the ASTNodeCompiler must create an ASTNodeValue representing the current value of this Species.

Specified by:

compile in interface ASTNodeCompiler

Returns:

cos

public ASTNodeValue cos(ASTNode value)
                 throws org.w3c.dom.DOMException,
                        SBMLException

Deprecated.

Specified by:

cos in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

cosh

public ASTNodeValue cosh(ASTNode value)
                  throws org.w3c.dom.DOMException,
                         SBMLException

Deprecated.

Specified by:

cosh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

cot

public ASTNodeValue cot(ASTNode value)
                 throws org.w3c.dom.DOMException,
                        SBMLException

Deprecated.

Specified by:

cot in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

coth

public ASTNodeValue coth(ASTNode value)
                  throws org.w3c.dom.DOMException,
                         SBMLException

Deprecated.

Specified by:

coth in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

createApplyNode

private ASTNodeValue createApplyNode(org.w3c.dom.Node tag,
                                     ASTNodeValue... childNodes)
                              throws org.w3c.dom.DOMException,
                                     SBMLException

Deprecated.

Parameters:

tag -

childNodes -

Returns:

Throws:

org.w3c.dom.DOMException

SBMLException

createApplyNode

private ASTNodeValue createApplyNode(org.w3c.dom.Node tag,
                                     java.util.List<ASTNode> childNodes)
                              throws org.w3c.dom.DOMException,
                                     SBMLException

Deprecated.

Creates an apply Node with the given tag Node as its child and ASTNodeValues on the same level as the tag Node .

Parameters:

tag -

childNodes -

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

createApplyNode

private ASTNodeValue createApplyNode(java.lang.String tagName,
                                     ASTNode... childNodes)
                              throws org.w3c.dom.DOMException,
                                     SBMLException

Deprecated.

Parameters:

tagName -

childNodes -

Returns:

Throws:

org.w3c.dom.DOMException

SBMLException

createApplyNode

private ASTNodeValue createApplyNode(java.lang.String tagName,
                                     ASTNodeValue... childNodes)
                              throws org.w3c.dom.DOMException,
                                     SBMLException

Deprecated.

Parameters:

tagName -

childNodes -

Returns:

Throws:

org.w3c.dom.DOMException

SBMLException

createApplyNode

private ASTNodeValue createApplyNode(java.lang.String tagName,
                                     java.util.List<ASTNode> childNodes)
                              throws org.w3c.dom.DOMException,
                                     SBMLException

Deprecated.

Creates a Node with the tag "apply" and adds the given Node as its child. Then it creates a new ASTNodeValue that wraps the apply Node.

Parameters:

tagName - The name of the node to be created, e.g., "abs" or "and".

childNodes - at least one child should be passed to this method.

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

createCiElement

private ASTNodeValue createCiElement(java.lang.String name)

Deprecated.

Parameters:

name -

Returns:

createCnElement

private org.w3c.dom.Element createCnElement(double mantissa,
                                            int exponent,
                                            java.lang.String units)

Deprecated.

Parameters:

mantissa -

exponent -

units - Can be null.

Returns:

createCnElement

private org.w3c.dom.Element createCnElement(java.lang.Number value,
                                            java.lang.String units)

Deprecated.

Parameters:

value -

units - Can be null.

Returns:

createConstant

private ASTNodeValue createConstant(java.lang.String tagName)

Deprecated.

Creates an ASTNodeValue with the single node as defined by the tagName.

Parameters:

tagName -

Returns:

createCSymbol

private org.w3c.dom.Element createCSymbol(java.lang.String name,
                                          java.lang.String definitionURI)

Deprecated.

Parameters:

name -

definitionURI -

Returns:

csc

public ASTNodeValue csc(ASTNode value)
                 throws org.w3c.dom.DOMException,
                        SBMLException

Deprecated.

Specified by:

csc in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

csch

public ASTNodeValue csch(ASTNode value)
                  throws org.w3c.dom.DOMException,
                         SBMLException

Deprecated.

Specified by:

csch in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

delay

public ASTNodeValue delay(java.lang.String delayName,
                          ASTNode x,
                          ASTNode delay,
                          java.lang.String timeUnit)
                   throws org.w3c.dom.DOMException,
                          SBMLException

Deprecated.

Description copied from interface: ASTNodeCompiler

Evaluates delay functions.

Specified by:

delay in interface ASTNodeCompiler

Parameters:

delayName - the name of this delay function.

delay - an expression of a positive duration time (the amoutn of delay)

timeUnit - the units for the delay.

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

eq

public ASTNodeValue eq(ASTNode left,
                       ASTNode right)
                throws org.w3c.dom.DOMException,
                       SBMLException

Deprecated.

Description copied from interface: ASTNodeCompiler

Equal.

Specified by:

eq in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

exp

public ASTNodeValue exp(ASTNode value)
                 throws org.w3c.dom.DOMException,
                        SBMLException

Deprecated.

Specified by:

exp in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

factorial

public ASTNodeValue factorial(ASTNode value)
                       throws org.w3c.dom.DOMException,
                              SBMLException

Deprecated.

Specified by:

factorial in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

floor

public ASTNodeValue floor(ASTNode value)
                   throws org.w3c.dom.DOMException,
                          SBMLException

Deprecated.

Specified by:

floor in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

frac

public ASTNodeValue frac(ASTNode numerator,
                         ASTNode denominator)
                  throws org.w3c.dom.DOMException,
                         SBMLException

Deprecated.

Description copied from interface: ASTNodeCompiler

Fraction of two ASTNodes

Specified by:

frac in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

frac

public ASTNodeValue frac(int numerator,
                         int denominator)
                  throws org.w3c.dom.DOMException,
                         SBMLException

Deprecated.

Description copied from interface: ASTNodeCompiler

A fraction of two int values.

Specified by:

frac in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

function

public ASTNodeValue function(FunctionDefinition functionDefinition,
                             java.util.List<ASTNode> args)
                      throws org.w3c.dom.DOMException,
                             SBMLException

Deprecated.

Specified by:

function in interface ASTNodeCompiler

args - Values to be inserted into the parameter list of the function.

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

function

public ASTNodeValue function(java.lang.String functionDefinitionName,
                             java.util.List<ASTNode> args)
                      throws SBMLException

Deprecated.

Specified by:

function in interface ASTNodeCompiler

args - Values to be inserted into the parameter list of the function.

Returns:

Throws:

SBMLException

geq

public ASTNodeValue geq(ASTNode left,
                        ASTNode right)
                 throws org.w3c.dom.DOMException,
                        SBMLException

Deprecated.

Description copied from interface: ASTNodeCompiler

Greater equal.

Specified by:

geq in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

getConstantAvogadro

public ASTNodeValue getConstantAvogadro(java.lang.String name)

Deprecated.

Description copied from interface: ASTNodeCompiler

Creates an ASTNodeValue that represent's Avogadro's number. Optionally, the compiler may associate the given name with this number.

Specified by:

getConstantAvogadro in interface ASTNodeCompiler

Parameters:

name - An optional name for Avogadro's number.

Returns:

getConstantE

public ASTNodeValue getConstantE()

Deprecated.

Specified by:

getConstantE in interface ASTNodeCompiler

Returns:

getConstantFalse

public ASTNodeValue getConstantFalse()

Deprecated.

Specified by:

getConstantFalse in interface ASTNodeCompiler

Returns:

getConstantPi

public ASTNodeValue getConstantPi()

Deprecated.

Specified by:

getConstantPi in interface ASTNodeCompiler

Returns:

getConstantTrue

public ASTNodeValue getConstantTrue()

Deprecated.

Specified by:

getConstantTrue in interface ASTNodeCompiler

Returns:

getDocument

public org.w3c.dom.Document getDocument()
                                 throws SBMLException

Deprecated.

Returns:

the document

Throws:

SBMLException

getLevel

public int getLevel()

Deprecated.

Returns:

the level

getNegativeInfinity

public ASTNodeValue getNegativeInfinity()
                                 throws org.w3c.dom.DOMException,
                                        SBMLException

Deprecated.

Specified by:

getNegativeInfinity in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

getPositiveInfinity

public ASTNodeValue getPositiveInfinity()

Deprecated.

Specified by:

getPositiveInfinity in interface ASTNodeCompiler

Returns:

gt

public ASTNodeValue gt(ASTNode left,
                       ASTNode right)
                throws org.w3c.dom.DOMException,
                       SBMLException

Deprecated.

Description copied from interface: ASTNodeCompiler

Greater than.

Specified by:

gt in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

init

private void init()
           throws javax.xml.stream.XMLStreamException

Deprecated.

Re-initializes the Document object belonging to this class. Only in this way a new ASTNode tree can be compiled. To this end, also the level attribute is reset (because maybe next time we want to compile some ASTNode with from a different source.

Throws:

javax.xml.stream.XMLStreamException

lambda

public ASTNodeValue lambda(java.util.List<ASTNode> values)
                    throws org.w3c.dom.DOMException,
                           SBMLException

Deprecated.

Description copied from interface: ASTNodeCompiler

The body of a FunctionDefinition.

Specified by:

lambda in interface ASTNodeCompiler

Parameters:

values - Place holders for arguments.

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

leq

public ASTNodeValue leq(ASTNode left,
                        ASTNode right)
                 throws org.w3c.dom.DOMException,
                        SBMLException

Deprecated.

Description copied from interface: ASTNodeCompiler

Less equal.

Specified by:

leq in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

ln

public ASTNodeValue ln(ASTNode value)
                throws org.w3c.dom.DOMException,
                       SBMLException

Deprecated.

Description copied from interface: ASTNodeCompiler

Natural logarithm.

Specified by:

ln in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

log

public ASTNodeValue log(ASTNode value)
                 throws org.w3c.dom.DOMException,
                        SBMLException

Deprecated.

Description copied from interface: ASTNodeCompiler

Logarithm of the given value to base 10.

Specified by:

log in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

log

public ASTNodeValue log(ASTNode base,
                        ASTNode value)
                 throws org.w3c.dom.DOMException,
                        SBMLException

Deprecated.

Description copied from interface: ASTNodeCompiler

Logarithm of the given value to the given base.

Specified by:

log in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

lt

public ASTNodeValue lt(ASTNode left,
                       ASTNode right)
                throws org.w3c.dom.DOMException,
                       SBMLException

Deprecated.

Description copied from interface: ASTNodeCompiler

Less than.

Specified by:

lt in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

minus

public ASTNodeValue minus(java.util.List<ASTNode> values)
                   throws org.w3c.dom.DOMException,
                          SBMLException

Deprecated.

Description copied from interface: ASTNodeCompiler

Subtraction.

Specified by:

minus in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

neq

public ASTNodeValue neq(ASTNode left,
                        ASTNode right)
                 throws org.w3c.dom.DOMException,
                        SBMLException

Deprecated.

Description copied from interface: ASTNodeCompiler

Not equal.

Specified by:

neq in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

not

public ASTNodeValue not(ASTNode value)
                 throws org.w3c.dom.DOMException,
                        SBMLException

Deprecated.

Specified by:

not in interface ASTNodeCompiler

Parameters:

value - This value must be interpretable as a Boolean.

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

or

public ASTNodeValue or(java.util.List<ASTNode> values)
                throws org.w3c.dom.DOMException,
                       SBMLException

Deprecated.

Specified by:

or in interface ASTNodeCompiler

Parameters:

values - These values must be interpretable as a Boolean.

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

piecewise

public ASTNodeValue piecewise(java.util.List<ASTNode> values)
                       throws org.w3c.dom.DOMException,
                              SBMLException

Deprecated.

Specified by:

piecewise in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

plus

public ASTNodeValue plus(java.util.List<ASTNode> values)
                  throws org.w3c.dom.DOMException,
                         SBMLException

Deprecated.

Specified by:

plus in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

pow

public ASTNodeValue pow(ASTNode base,
                        ASTNode exponent)
                 throws org.w3c.dom.DOMException,
                        SBMLException

Deprecated.

Specified by:

pow in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

reset

public void reset()
           throws javax.xml.stream.XMLStreamException

Deprecated.

Allows to re-use this object to compile another ASTNode. Without reseting, this compiler can only be used one time. Otherwise it cannot be guaranteed that the results will be correct.

Throws:

javax.xml.stream.XMLStreamException

root

public ASTNodeValue root(ASTNode rootExponent,
                         ASTNode radiant)
                  throws org.w3c.dom.DOMException,
                         SBMLException

Deprecated.

Specified by:

root in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

root

private ASTNodeValue root(ASTNodeValue rootExponent,
                          ASTNode radiant)
                   throws org.w3c.dom.DOMException,
                          SBMLException

Deprecated.

Parameters:

rootExponent -

radiant -

Returns:

Throws:

org.w3c.dom.DOMException

SBMLException

root

public ASTNodeValue root(double rootExponent,
                         ASTNode radiant)
                  throws org.w3c.dom.DOMException,
                         SBMLException

Deprecated.

Specified by:

root in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

sec

public ASTNodeValue sec(ASTNode value)
                 throws org.w3c.dom.DOMException,
                        SBMLException

Deprecated.

Specified by:

sec in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

sech

public ASTNodeValue sech(ASTNode value)
                  throws org.w3c.dom.DOMException,
                         SBMLException

Deprecated.

Specified by:

sech in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

setLevel

private void setLevel(int level)

Deprecated.

Parameters:

level - the level to set

sin

public ASTNodeValue sin(ASTNode value)
                 throws org.w3c.dom.DOMException,
                        SBMLException

Deprecated.

Specified by:

sin in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

sinh

public ASTNodeValue sinh(ASTNode value)
                  throws org.w3c.dom.DOMException,
                         SBMLException

Deprecated.

Specified by:

sinh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

sqrt

public ASTNodeValue sqrt(ASTNode value)
                  throws org.w3c.dom.DOMException,
                         SBMLException

Deprecated.

Description copied from interface: ASTNodeCompiler

Square root.

Specified by:

sqrt in interface ASTNodeCompiler

Parameters:

value - This value must be interpretable as a Number.

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

symbolTime

public ASTNodeValue symbolTime(java.lang.String time)

Deprecated.

Description copied from interface: ASTNodeCompiler

The simulation time.

Specified by:

symbolTime in interface ASTNodeCompiler

Parameters:

time - The name of the time symbol.

Returns:

An ASTNodeValue that represents the current time.

tan

public ASTNodeValue tan(ASTNode value)
                 throws org.w3c.dom.DOMException,
                        SBMLException

Deprecated.

Specified by:

tan in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

tanh

public ASTNodeValue tanh(ASTNode value)
                  throws org.w3c.dom.DOMException,
                         SBMLException

Deprecated.

Specified by:

tanh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

times

private ASTNodeValue times(ASTNodeValue... values)
                    throws org.w3c.dom.DOMException,
                           SBMLException

Deprecated.

Convenient method to perform internal changes.

Parameters:

values -

Returns:

Throws:

org.w3c.dom.DOMException

SBMLException

times

public ASTNodeValue times(java.util.List<ASTNode> values)
                   throws org.w3c.dom.DOMException,
                          SBMLException

Deprecated.

Description copied from interface: ASTNodeCompiler

Product of all given ASTNodes.

Specified by:

times in interface ASTNodeCompiler

Parameters:

values - These values must be interpretable to Number.

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

toMathML

public java.lang.String toMathML(boolean omitXMLDeclaration,
                                 boolean indenting,
                                 int indent)
                          throws java.io.IOException,
                                 SBMLException

Deprecated.

Parameters:

omitXMLDeclaration -

indenting -

indent -

Returns:

Throws:

java.io.IOException

SBMLException

uMinus

public ASTNodeValue uMinus(ASTNode value)
                    throws org.w3c.dom.DOMException,
                           SBMLException

Deprecated.

Description copied from interface: ASTNodeCompiler

Unary minus, i.e., negation of the given ASTNode.

Specified by:

uMinus in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

uMinus

private ASTNodeValue uMinus(ASTNodeValue value)
                     throws org.w3c.dom.DOMException,
                            SBMLException

Deprecated.

Parameters:

value -

Returns:

Throws:

org.w3c.dom.DOMException

SBMLException

unknownValue

public ASTNodeValue unknownValue()
                          throws SBMLException

Deprecated.

Description copied from interface: ASTNodeCompiler

Dealing with a malformed ASTNode.

Specified by:

unknownValue in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

writeName

private java.lang.String writeName(java.lang.Object name)

Deprecated.

Converts the given Object into a String. Then it removes leading and tailing white spaces from the given String and then inserts exactly one white space at the beginning and the end of the given String.

Parameters:

name -

Returns:

xor

public ASTNodeValue xor(java.util.List<ASTNode> values)
                 throws org.w3c.dom.DOMException,
                        SBMLException

Deprecated.

Description copied from interface: ASTNodeCompiler

Exclusive or.

Specified by:

xor in interface ASTNodeCompiler

Parameters:

values - It must be possible to evaluate the given values to Boolean.

Returns:

Throws:

SBMLException

org.w3c.dom.DOMException

selector

public ASTNodeValue selector(java.util.List<ASTNode> nodes)
                      throws SBMLException

Deprecated.

Specified by:

selector in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

vector

public ASTNodeValue vector(java.util.List<ASTNode> nodes)
                    throws SBMLException

Deprecated.

Description copied from interface: ASTNodeCompiler

Dealing with a vector.

Specified by:

vector in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

max

public ASTNodeValue max(java.util.List<ASTNode> values)

Deprecated.

Description copied from interface: ASTNodeCompiler

Returns the maximum of the values.

Specified by:

max in interface ASTNodeCompiler

Returns:

the maximum of the values.

min

public ASTNodeValue min(java.util.List<ASTNode> values)

Deprecated.

Description copied from interface: ASTNodeCompiler

Returns the minimum of the values.

Specified by:

min in interface ASTNodeCompiler

Returns:

the minimum of the values.

quotient

public ASTNodeValue quotient(java.util.List<ASTNode> values)

Deprecated.

Description copied from interface: ASTNodeCompiler

Returns the quotient of the division of the values.

Specified by:

quotient in interface ASTNodeCompiler

Returns:

the quotient of the values.

rem

public ASTNodeValue rem(java.util.List<ASTNode> values)

Deprecated.

Description copied from interface: ASTNodeCompiler

Returns the remainder of the division of the values.

Specified by:

rem in interface ASTNodeCompiler

Returns:

the remainder of the division of the values.

implies

public ASTNodeValue implies(java.util.List<ASTNode> values)

Deprecated.

Description copied from interface: ASTNodeCompiler

Returns the logical implies between two ASTNode.

Truth table:

 p   q  p→q
 
 T   T   T
 T   F   F
 F   T   T
 F   F   T

Specified by:

implies in interface ASTNodeCompiler

Returns:

the logical implies between two ASTNode.

getRateOf

public ASTNodeValue getRateOf(java.lang.String name)

Deprecated.

Specified by:

getRateOf in interface ASTNodeCompiler

Returns: